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dberkholz 08/08/03 07:54:01 |
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|
| 3 |
Modified: ChangeLog metadata.xml |
| 4 |
Added: cns-1.2.1.ebuild |
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Log: |
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Bump. Keyword ~amd64; add OpenMP support for parallel refinement; (#209805) Fix a number of environment variables and cns_ functions to work properly. |
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(Portage version: 2.2_rc5/cvs/Linux 2.6.26 x86_64) |
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|
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Revision Changes Path |
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1.11 sci-chemistry/cns/ChangeLog |
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|
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file : http://sources.gentoo.org/viewcvs.py/gentoo-x86/sci-chemistry/cns/ChangeLog?rev=1.11&view=markup |
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plain: http://sources.gentoo.org/viewcvs.py/gentoo-x86/sci-chemistry/cns/ChangeLog?rev=1.11&content-type=text/plain |
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diff : http://sources.gentoo.org/viewcvs.py/gentoo-x86/sci-chemistry/cns/ChangeLog?r1=1.10&r2=1.11 |
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|
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Index: ChangeLog |
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=================================================================== |
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RCS file: /var/cvsroot/gentoo-x86/sci-chemistry/cns/ChangeLog,v |
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retrieving revision 1.10 |
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retrieving revision 1.11 |
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diff -u -r1.10 -r1.11 |
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--- ChangeLog 3 Jun 2008 02:09:01 -0000 1.10 |
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+++ ChangeLog 3 Aug 2008 07:54:00 -0000 1.11 |
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@@ -1,6 +1,15 @@ |
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# ChangeLog for sci-chemistry/cns |
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# Copyright 1999-2008 Gentoo Foundation; Distributed under the GPL v2 |
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-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/cns/ChangeLog,v 1.10 2008/06/03 02:09:01 mr_bones_ Exp $ |
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+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/cns/ChangeLog,v 1.11 2008/08/03 07:54:00 dberkholz Exp $ |
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+ |
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+*cns-1.2.1 (03 Aug 2008) |
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+ |
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+ 03 Aug 2008; Donnie Berkholz <dberkholz@g.o>; |
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+ +files/1.2.1-allow-gcc-openmp.patch, +files/cns_solve_env_sh, |
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+ metadata.xml, +cns-1.2.1.ebuild: |
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+ Bump. Keyword ~amd64; add OpenMP support for parallel refinement; |
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+ (#209805) Fix a number of environment variables and cns_ functions to work |
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+ properly. |
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|
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03 Jun 2008; Michael Sterrett <mr_bones_@g.o> cns-1.1.ebuild, |
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cns-1.2.ebuild, cns-1.2-r1.ebuild: |
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|
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|
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|
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1.5 sci-chemistry/cns/metadata.xml |
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|
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file : http://sources.gentoo.org/viewcvs.py/gentoo-x86/sci-chemistry/cns/metadata.xml?rev=1.5&view=markup |
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plain: http://sources.gentoo.org/viewcvs.py/gentoo-x86/sci-chemistry/cns/metadata.xml?rev=1.5&content-type=text/plain |
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diff : http://sources.gentoo.org/viewcvs.py/gentoo-x86/sci-chemistry/cns/metadata.xml?r1=1.4&r2=1.5 |
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|
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Index: metadata.xml |
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=================================================================== |
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RCS file: /var/cvsroot/gentoo-x86/sci-chemistry/cns/metadata.xml,v |
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retrieving revision 1.4 |
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retrieving revision 1.5 |
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diff -u -r1.4 -r1.5 |
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--- metadata.xml 20 Sep 2006 05:08:59 -0000 1.4 |
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+++ metadata.xml 3 Aug 2008 07:54:00 -0000 1.5 |
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@@ -2,4 +2,7 @@ |
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<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> |
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<pkgmetadata> |
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<herd>sci-chemistry</herd> |
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+<use> |
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+ <flag name='openmp'>Build support for the OpenMP (support parallel computing)</flag> |
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+</use> |
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</pkgmetadata> |
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|
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|
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|
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1.1 sci-chemistry/cns/cns-1.2.1.ebuild |
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|
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file : http://sources.gentoo.org/viewcvs.py/gentoo-x86/sci-chemistry/cns/cns-1.2.1.ebuild?rev=1.1&view=markup |
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plain: http://sources.gentoo.org/viewcvs.py/gentoo-x86/sci-chemistry/cns/cns-1.2.1.ebuild?rev=1.1&content-type=text/plain |
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|
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Index: cns-1.2.1.ebuild |
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=================================================================== |
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# Copyright 1999-2008 Gentoo Foundation |
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# Distributed under the terms of the GNU General Public License v2 |
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# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/cns/cns-1.2.1.ebuild,v 1.1 2008/08/03 07:54:00 dberkholz Exp $ |
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|
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inherit eutils fortran toolchain-funcs versionator flag-o-matic |
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|
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MY_PN="${PN}_solve" |
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MY_PV="$(delete_version_separator 2)" |
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MY_P="${MY_PN}_${MY_PV}" |
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|
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DESCRIPTION="Crystallography and NMR System" |
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HOMEPAGE="http://cns.csb.yale.edu/" |
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SRC_URI="!openmp? ( ${MY_P}_all.tar.gz ) |
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openmp? ( ${MY_P}_all-mp.tar.gz )" |
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RESTRICT="fetch" |
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LICENSE="cns" |
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SLOT="0" |
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KEYWORDS="~amd64 ~ppc ~x86" |
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IUSE="openmp" |
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RDEPEND="app-shells/tcsh |
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!app-text/dos2unix" |
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DEPEND="${RDEPEND}" |
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S="${WORKDIR}/${MY_P}" |
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|
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FORTRAN="g77 gfortran" |
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|
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pkg_nofetch() { |
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einfo "Fill out the form at http://cns.csb.yale.edu/cns_request/" |
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einfo "and place these files:" |
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einfo "${A}" |
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einfo "in ${DISTDIR}." |
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} |
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|
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pkg_setup() { |
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fortran_pkg_setup |
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|
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if use openmp; then |
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if [[ gcc-major-version < 4 ]] \ |
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|| ( [[ gcc-major-version < 4 ]] && [[ gcc-minor-version < 2 ]] ); then |
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local msg="Sorry, you need gcc 4.2 or newer to use OpenMP." |
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eerror "$msg" |
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die "$msg" |
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fi |
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fi |
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} |
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|
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src_unpack() { |
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unpack ${A} |
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cd "${S}" |
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|
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use openmp && append-flags -fopenmp |
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use openmp && append-ldflags -lgomp |
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|
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# Someone already did the same in the openmp version, apparently |
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use openmp || epatch "${FILESDIR}"/1.2-allow-unknown-architectures.patch |
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|
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# the code uses Intel-compiler-specific directives |
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use openmp && epatch "${FILESDIR}"/${PV}-allow-gcc-openmp.patch |
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|
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# Set up location for the build directory |
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# Uses obsolete `sort` syntax, so we set _POSIX2_VERSION |
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cp "${FILESDIR}"/cns_solve_env_sh "${T}"/ |
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sed -i \ |
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-e "s:_CNSsolve_location_:${S}:g" \ |
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-e "17 s:\(.*\):\1\nsetenv _POSIX2_VERSION 199209:g" \ |
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"${S}"/cns_solve_env |
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sed -i \ |
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-e "s:_CNSsolve_location_:${S}:g" \ |
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-e "17 s:\(.*\):\1\nexport _POSIX2_VERSION; _POSIX2_VERSION=199209:g" \ |
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"${T}"/cns_solve_env_sh |
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} |
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|
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src_compile() { |
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local GLOBALS |
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local MALIGN= |
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if [[ ${FORTRANC} = g77 ]]; then |
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GLOBALS="-fno-globals" |
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MALIGN='\$(CNS_MALIGN_I86)' |
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fi |
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|
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# Set up the compiler to use |
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pushd instlib/machine/unsupported/g77-unix 2>/dev/null |
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ln -s Makefile.header Makefile.header.${FORTRANC} || die |
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popd 2>/dev/null |
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|
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# make install really means build, since it's expected to be used in-place |
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emake \ |
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CC="$(tc-getCC)" \ |
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F77="${FORTRANC}" \ |
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LD="${FORTRANC}" \ |
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CCFLAGS="${CFLAGS} -DCNS_ARCH_TYPE_\$(CNS_ARCH_TYPE) \$(EXT_CCFLAGS)" \ |
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LDFLAGS="${LDFLAGS}" \ |
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F77OPT="${FFLAGS:- -O2} ${MALIGN}" \ |
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F77STD="${GLOBALS}" \ |
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g77install \ |
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|| die "emake failed" |
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} |
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|
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src_test() { |
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# We need to force on g77 manually, because we can't get aliases working |
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# when we source in a -c |
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einfo "Running tests ..." |
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sh -c \ |
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"export CNS_G77=ON; source .cns_solve_env_sh; make run_tests" \ |
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|| die "tests failed" |
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einfo "Displaying test results ..." |
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cat "${S}"/*_g77/test/*.diff-test |
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} |
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|
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src_install() { |
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# Install to locations resembling FHS |
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sed -i \ |
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-e "s:${S}:usr:g" \ |
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-e "s:^\(setenv CNS_SOLVE.*\):\1\nsetenv CNS_ROOT usr:g" \ |
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-e "s:^\(setenv CNS_SOLVE.*\):\1\nsetenv CNS_DATA \$CNS_ROOT/share/data:g" \ |
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-e "s:^\(setenv CNS_SOLVE.*\):\1\nsetenv CNS_DOC \$CNS_ROOT/share/doc/${PF}:g" \ |
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-e "s:CNS_LIB \$CNS_SOLVE/libraries:CNS_LIB \$CNS_DATA/libraries:g" \ |
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-e "s:CNS_MODULE \$CNS_SOLVE/modules:CNS_MODULE \$CNS_DATA/modules:g" \ |
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-e "s:CNS_HELPLIB \$CNS_SOLVE/helplib:CNS_HELPLIB \$CNS_DATA/helplib:g" \ |
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-e "s:\$CNS_SOLVE/bin/cns_info:\$CNS_DATA/cns_info:g" \ |
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"${S}"/cns_solve_env |
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# I don't entirely understand why the sh version requires a leading / |
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# for CNS_SOLVE and CNS_ROOT, but it does |
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sed -i \ |
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-e "s:${S}:/usr:g" \ |
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-e "s:^\(^[[:space:]]*CNS_SOLVE=.*\):\1\nexport CNS_ROOT=/usr:g" \ |
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-e "s:^\(^[[:space:]]*CNS_SOLVE=.*\):\1\nexport CNS_DATA=\$CNS_ROOT/share/cns:g" \ |
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-e "s:^\(^[[:space:]]*CNS_SOLVE=.*\):\1\nexport CNS_DOC=\$CNS_ROOT/share/doc/${PF}:g" \ |
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-e "s:CNS_LIB=\$CNS_SOLVE/libraries:CNS_LIB=\$CNS_DATA/libraries:g" \ |
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-e "s:CNS_MODULE=\$CNS_SOLVE/modules:CNS_MODULE=\$CNS_DATA/modules:g" \ |
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-e "s:CNS_HELPLIB=\$CNS_SOLVE/helplib:CNS_HELPLIB=\$CNS_DATA/helplib:g" \ |
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-e "s:\$CNS_SOLVE/bin/cns_info:\$CNS_DATA/cns_info:g" \ |
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"${T}"/cns_solve_env_sh |
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|
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# Get rid of setup stuff we don't need in the installed script |
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sed -i \ |
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-e "83,$ d" \ |
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-e "37,46 d" \ |
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"${S}"/cns_solve_env |
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sed -i \ |
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-e "84,$ d" \ |
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-e "39,50 d" \ |
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"${T}"/cns_solve_env_sh |
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|
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newbin "${S}"/*_g77/bin/cns_solve* cns_solve \ |
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|| die "install cns_solve failed" |
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|
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# Can be run by either cns_solve or cns |
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dosym cns_solve /usr/bin/cns |
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|
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# Don't want to install this |
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rm -f "${S}"/*_g77/utils/Makefile |
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|
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dobin "${S}"/*_g77/utils/* || die "install utils failed" |
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|
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sed -i \ |
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-e "s:\$CNS_SOLVE/doc/:\$CNS_SOLVE/share/doc/${PF}/:g" \ |
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"${S}"/bin/cns_web |
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|
| 235 |
dobin "${S}"/bin/cns_{edit,header,transfer,web} || die "install bin failed" |
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|
| 237 |
insinto /usr/share/cns |
| 238 |
doins -r "${S}"/libraries "${S}"/modules "${S}"/helplib |
| 239 |
doins "${S}"/bin/cns_info |
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|
| 241 |
insinto /etc/profile.d |
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newins "${S}"/cns_solve_env cns_solve_env.csh |
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newins "${T}"/cns_solve_env_sh cns_solve_env.sh |
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|
| 245 |
dohtml \ |
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-A iq,cgi,csh,cv,def,fm,gif,hkl,inp,jpeg,lib,link,list,mask,mtf,param,pdb,pdf,pl,ps,sc,sca,sdb,seq,tbl,top \ |
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-f all_cns_info_template,omac,def \ |
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-r doc/html/* |
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} |
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|
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pkg_info() { |
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if use openmp; then |
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elog "Set OMP_NUM_THREADS to the number of threads you want." |
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elog "If you get segfaults on large structures, set the GOMP_STACKSIZE" |
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elog "variable if using gcc (16384 should be good). Also run" |
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elog "ulimit -s 16384." |
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fi |
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} |
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|
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pkg_postinst() { |
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pkg_info |
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} |
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